The performance of Fourier transform infrared spectroscopy (FT-IR) detection coupled to high-performance liquid chromatography for the analysis of C60 and C70 fullerenes was investigated. The isocratic separation method involved an octadecylsilane (ODS) column and an acetonitrile-toluene (1:1) mobile phase. The hyphenated system was designed with a split valve to control eluent volume leading to the FT-IR detector; this allowed for additional coupling of the liquid chromatograph to ultraviolet-visible detection. On-line FT-IR spectra of C60 and C70 were matched with standard off-line FT-IR spectra from the literature. In addition, with band chromatograms individual fullerenes can be identified using FT-IR active modes known specifically for each fullerene. Few changes to a pre-existing HPLC-UV method were necessary for the HPLC-FT-IR method, and there was no need for fraction collection to identify the fullerenes C60 and C70.